[Freesurfer] Convert sig.cluster.mgh file to a binary mask in .nii format

External Email - Use Caution Dear FreeSurfer users, I am trying to extract a binary mask from the file cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and convert this mask into a .nii file. I have found a previous message in the forum that reccomends using

[Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

External Email - Use Caution Dear FreeSurfer users, I am trying to run the Thalamic nuclei and the hippocampal/amygdala segmentation scripts but there is an error with the matlab license. The error message is: LD_LIBRARY_PATH is .:/nas01/users/carme/freesurfer/MCRv84//runtime/gln

[Freesurfer] motion parameter in preprocessing stream

Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Great! Thanks! 2018-01-08 16:44 GMT+01:00 Hoopes, Andrew : > Hi Carme, > > segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh. > harvard.edu/pub/dist/freesurfer/dev > > best, > Andrew > > > On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal >

[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Dear FreeSurfer users, I wanted to run the new script that segments the hippocampus and amygdala (segmentHA_T1.sh: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) but I can't find it in FreeSurfer 6.0. Is it already available? Where can I find it? Thanks in adv

Re: [Freesurfer] Merge both hemispheres in cortical parcellations

) * > (rh_average_thick)) > -- > nvertices_lh + nvertices_rh > > cheers > Bruce > > > On Thu, 17 > Dec 2015, Carme Uribe Codesal wrote: > > > Dear FreeSurfer users, > > > > I've been looking for an approp

[Freesurfer] Merge both hemispheres in cortical parcellations

Dear FreeSurfer users, I've been looking for an appropiate way to merge both hemispheres in the Desikan parcellations but I can't find it in the list. Which formula do I need to use to consider, for example, the bilateral posterior cingulate as an only measure (not lh and rh separated)? I'm not

[Freesurfer] error in mri_glmfit-sim using a per-vertex regressor

Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_M